[Debian-med-packaging] Bug#957431: libbpp-seq-omics: ftbfs with GCC-10

Fri Apr 17 12:04:08 BST 2020

Package: src:libbpp-seq-omics
Version: 2.4.1-4
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-10

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-10/g++-10, but succeeds to build with gcc-9/g++-9. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc10-20200225/libbpp-seq-omics_2.4.1-4_unstable_gcc10.log
The last lines of the build log are at the end of this report.

To build with GCC 10, either set CC=gcc-10 CXX=g++-10 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-10/porting_to.html

[...]
- _ZNSt8_Rb_treeIPN3bpp5RangeImEES3_St9_IdentityIS3_ENS0_10rangeComp_ImEESaIS3_EE8_M_eraseEPSt13_Rb_tree_nodeIS3_E at Base 2.4.1
+#MISSING: 2.4.1-4# _ZNSt8_Rb_treeIPN3bpp5RangeImEES3_St9_IdentityIS3_ENS0_10rangeComp_ImEESaIS3_EE8_M_eraseEPSt13_Rb_tree_nodeIS3_E at Base 2.4.1
  _ZNSt8_Rb_treeIcSt4pairIKcSt3mapImS2_ImmSt4lessImESaIS0_IKmmEEES4_SaIS0_IS5_S8_EEEESt10_Select1stISC_ES3_IcESaISC_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeIcSt4pairIKcSt3mapImS2_ImmSt4lessImESaIS0_IKmmEEES4_SaIS0_IS5_S8_EEEESt10_Select1stISC_ES3_IcESaISC_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorISC_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIcSt4pairIKcSt3mapImS2_ImmSt4lessImESaIS0_IKmmEEES4_SaIS0_IS5_S8_EEEESt10_Select1stISC_ES3_IcESaISC_EE8_M_eraseEPSt13_Rb_tree_nodeISC_E at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessIiESaIS8_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESJ_IJEEEEESt17_Rb_tree_iteratorIS8_ESt23_Rb_tree_const_iteratorIS8_EDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-4# _ZNSt8_Rb_treeIcSt4pairIKcSt3mapImS2_ImmSt4lessImESaIS0_IKmmEEES4_SaIS0_IS5_S8_EEEESt10_Select1stISC_ES3_IcESaISC_EE8_M_eraseEPSt13_Rb_tree_nodeISC_E at Base 2.4.1
+#MISSING: 2.4.1-4# _ZNSt8_Rb_treeIiSt4pairIKiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessIiESaIS8_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESJ_IJEEEEESt17_Rb_tree_iteratorIS8_ESt23_Rb_tree_const_iteratorIS8_EDpOT_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessIiESaIS8_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessIiESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessIiESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E at Base 2.4.1
+#MISSING: 2.4.1-4# _ZNSt8_Rb_treeIiSt4pairIKiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessIiESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE14_M_insert_nodeEPSt18_Rb_tree_node_baseSA_PSt13_Rb_tree_nodeIS2_E at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-4# _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 2.4.1
+#MISSING: 2.4.1-4# _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE14_M_insert_nodeEPSt18_Rb_tree_node_baseSA_PSt13_Rb_tree_nodeIS2_E at Base 2.4.1
+#MISSING: 2.4.1-4# _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKijESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKijESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKijESt10_Select1stIS2_ESt4lessIiESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-4# _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE7_M_copyINS8_11_Alloc_nodeEEEPSt13_Rb_tree_nodeIS2_EPKSC_PSt18_Rb_tree_node_baseRT_ at Base 2.4.1
+#MISSING: 2.4.1-4# _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE7_M_copyINS8_11_Alloc_nodeEEEPSt13_Rb_tree_nodeIS2_EPKSC_PSt18_Rb_tree_node_baseRT_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 2.4.1
+ _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EEC1ERKS8_ at Base 2.4.1-4
+ _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EEC2ERKS8_ at Base 2.4.1-4
  _ZNSt8_Rb_treeImSt4pairIKmSt3mapImmSt4lessImESaIS0_IS1_mEEEESt10_Select1stIS8_ES4_SaIS8_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeImSt4pairIKmSt3mapImmSt4lessImESaIS0_IS1_mEEEESt10_Select1stIS8_ES4_SaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeImSt4pairIKmSt3mapImmSt4lessImESaIS0_IS1_mEEEESt10_Select1stIS8_ES4_SaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E at Base 2.4.1
+#MISSING: 2.4.1-4# _ZNSt8_Rb_treeImSt4pairIKmSt3mapImmSt4lessImESaIS0_IS1_mEEEESt10_Select1stIS8_ES4_SaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E at Base 2.4.1
  _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 2.4.1
+#MISSING: 2.4.1-4# _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 2.4.1
  _ZSt11__make_heapIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops15_Iter_less_iterEEvT_SF_RT0_ at Base 2.4.1
- _ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEElS7_NS0_5__ops15_Iter_less_iterEEvT_T0_SG_T1_T2_ at Base 2.4.1
- _ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIPPN3bpp5RangeImEESt6vectorIS5_SaIS5_EEEElS5_NS0_5__ops15_Iter_comp_iterINS2_10rangeComp_ImEEEEEvT_T0_SH_T1_T2_ at Base 2.4.1
- _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops15_Iter_less_iterEEvT_SF_T0_ at Base 2.4.1
- _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPPN3bpp5RangeImEESt6vectorIS5_SaIS5_EEEENS0_5__ops15_Iter_comp_iterINS2_10rangeComp_ImEEEEEvT_SG_T0_ at Base 2.4.1
+#MISSING: 2.4.1-4# _ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEElS7_NS0_5__ops15_Iter_less_iterEEvT_T0_SG_T1_T2_ at Base 2.4.1
+#MISSING: 2.4.1-4# _ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIPPN3bpp5RangeImEESt6vectorIS5_SaIS5_EEEElS5_NS0_5__ops15_Iter_comp_iterINS2_10rangeComp_ImEEEEEvT_T0_SH_T1_T2_ at Base 2.4.1
+#MISSING: 2.4.1-4# _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops15_Iter_less_iterEEvT_SF_T0_ at Base 2.4.1
+#MISSING: 2.4.1-4# _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPPN3bpp5RangeImEESt6vectorIS5_SaIS5_EEEENS0_5__ops15_Iter_comp_iterINS2_10rangeComp_ImEEEEEvT_SG_T0_ at Base 2.4.1
+ _ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEElNS0_5__ops15_Iter_less_iterEEvT_SF_T0_T1_ at Base 2.4.1-4
  _ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIPPN3bpp5RangeImEESt6vectorIS5_SaIS5_EEEElNS0_5__ops15_Iter_comp_iterINS2_10rangeComp_ImEEEEEvT_SG_T0_T1_ at Base 2.4.1
- _ZSt25__unguarded_linear_insertIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops14_Val_less_iterEEvT_T0_ at Base 2.4.1
+#MISSING: 2.4.1-4# _ZSt25__unguarded_linear_insertIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops14_Val_less_iterEEvT_T0_ at Base 2.4.1
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_ at Base 2.4.1
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_S9_ at Base 2.4.1
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_OS8_ at Base 2.4.1
@@ -893,6 +940,7 @@
  _ZTVN3bpp6NumberIdEE at Base 2.4.1
  _ZTVN3bpp6NumberIiEE at Base 2.4.1
  _ZTVN3bpp6NumberIjEE at Base 2.4.1
+ _ZTVN3bpp8ClonableE at Base 2.4.1-4
  _ZTVN3bpp8MafBlockE at Base 2.4.1
  _ZTVN3bpp8RangeSetImEE at Base 2.4.1
  _ZTVN3bpp8SeqRangeE at Base 2.4.1
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:10: binary] Error 25
dpkg-buildpackage: error: fakeroot debian/rules binary subprocess returned exit status 2

